# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 14:11:25 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(azanyloxymethyl)oxolane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NOC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 DJ2  DJ2  (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(azanyloxymethyl)oxolane-3,4-diol  ligand  34  20  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DJ2
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 DJ2  C4   C  CR56  0   0.492   1.7962  -0.1338  -0.3152
 DJ2  C5   C  CR56  0  -0.012   2.4506   0.9839   0.1780
 DJ2  C6   C  CR6   0   0.460   3.8417   1.0339  -0.0282
 DJ2  C8   C  CR15  0   0.113   0.4134   1.2535   0.6585
 DJ2  N1   N  N     0  -0.475   4.4146   0.0164  -0.6816
 DJ2  N3   N  N     0  -0.456   2.3517  -1.1535  -0.9650
 DJ2  C1'  C  CH1   0   0.214  -0.6067  -0.8461  -0.2825
 DJ2  C2   C  CR16  0   0.046   3.6560  -0.9915  -1.1037
 DJ2  C2'  C  CH1   0  -0.049  -1.2481  -1.4569   0.9627
 DJ2  C3'  C  CH1   0  -0.034  -2.6623  -1.7504   0.4543
 DJ2  C4'  C  CH1   0  -0.054  -2.9115  -0.5431  -0.4415
 DJ2  C5'  C  CH2   0  -0.116  -3.5823   0.5922   0.3058
 DJ2  N6   N  NH2   0  -0.816   4.5989   2.0440   0.4003
 DJ2  N7   N  N     0  -0.449   1.5657   1.8407   0.7810
 DJ2  N9   N  NR5   0  -0.539   0.4821   0.0517   0.0063
 DJ2  NAA  N  NH2   0  -0.540  -4.3039   2.7624   0.0859
 DJ2  O2'  O  OH1   0  -0.652  -0.5215  -2.5770   1.3680
 DJ2  O3'  O  OH1   0  -0.668  -2.6817  -2.9104  -0.3356
 DJ2  O4'  O  O2    0  -0.490  -1.6265  -0.1425  -0.9312
 DJ2  O5'  O  O2    0  -0.430  -3.6903   1.6790  -0.5756
 DJ2  H1   H  HCR5  0   0.292  -0.5239   1.6550   1.0139
 DJ2  H2   H  HCH1  0   0.262  -0.1888  -1.6363  -0.9165
 DJ2  H3   H  HCR6  0   0.252   4.1819  -1.7812  -1.6293
 DJ2  H4   H  HCH1  0   0.251  -1.3032  -0.7025   1.7580
 DJ2  H5   H  HCH1  0   0.254  -3.3885  -1.8060   1.2758
 DJ2  H6   H  HCH1  0   0.265  -3.5317  -0.8239  -1.2984
 DJ2  H7   H  HCH2  0   0.217  -4.5681   0.2463   0.6410
 DJ2  H8   H  HCH2  0   0.197  -3.0143   0.8658   1.2060
 DJ2  H9   H  HNH2  0   0.412   4.1968   2.8276   0.8837
 DJ2  H10  H  HNH2  0   0.404   5.5873   2.0515   0.2170
 DJ2  H11  H  HNH2  0   0.365  -3.6534   3.5343  -0.0205
 DJ2  H12  H  HNH2  0   0.366  -5.1052   2.9993  -0.4901
 DJ2  H13  H  HOH1  0   0.470  -0.7352  -2.7732   2.2858
 DJ2  H14  H  HOH1  0   0.450  -2.1912  -3.5965   0.1320

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 DJ2  N6   C6   single    1.333  0.020  1.333
 DJ2  N7   C8   aromatic  1.299  0.020  1.299
 DJ2  N7   C5   aromatic  1.371  0.020  1.371
 DJ2  C6   C5   aromatic  1.407  0.020  1.407
 DJ2  C6   N1   aromatic  1.338  0.020  1.338
 DJ2  C8   N9   aromatic  1.369  0.020  1.369
 DJ2  C5   C4   aromatic  1.386  0.020  1.386
 DJ2  O4'  C4'  single    1.432  0.020  1.432
 DJ2  O4'  C1'  single    1.398  0.020  1.398
 DJ2  C5'  O5'  single    1.403  0.020  1.403
 DJ2  C5'  C4'  single    1.516  0.020  1.516
 DJ2  N1   C2   aromatic  1.330  0.020  1.330
 DJ2  NAA  O5'  single    1.410  0.020  1.410
 DJ2  N9   C4   aromatic  1.366  0.020  1.366
 DJ2  N9   C1'  single    1.441  0.020  1.441
 DJ2  C4   N3   aromatic  1.331  0.020  1.331
 DJ2  C4'  C3'  single    1.524  0.020  1.524
 DJ2  C2   N3   aromatic  1.322  0.020  1.322
 DJ2  C1'  C2'  single    1.528  0.020  1.528
 DJ2  C3'  C2'  single    1.531  0.020  1.531
 DJ2  C3'  O3'  single    1.404  0.020  1.404
 DJ2  C2'  O2'  single    1.395  0.020  1.395
 DJ2  C8   H1   single    0.930  0.020  1.080
 DJ2  C1'  H2   single    0.970  0.020  1.090
 DJ2  C2   H3   single    0.930  0.020  1.080
 DJ2  C2'  H4   single    0.970  0.020  1.090
 DJ2  C3'  H5   single    0.970  0.020  1.090
 DJ2  C4'  H6   single    0.970  0.020  1.090
 DJ2  C5'  H7   single    0.970  0.020  1.090
 DJ2  C5'  H8   single    0.970  0.020  1.090
 DJ2  N6   H9   single    0.860  0.020  1.020
 DJ2  N6   H10  single    0.860  0.020  1.020
 DJ2  NAA  H11  single    0.890  0.020  1.040
 DJ2  NAA  H12  single    0.890  0.020  1.040
 DJ2  O2'  H13  single    0.850  0.020  0.980
 DJ2  O3'  H14  single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 DJ2  N9   C4   N3   128.38  3.000
 DJ2  N3   C4   C5   126.49  3.000
 DJ2  N9   C4   C5   105.13  3.000
 DJ2  N7   C5   C6   132.85  3.000
 DJ2  C6   C5   C4   116.31  3.000
 DJ2  N7   C5   C4   110.84  3.000
 DJ2  N6   C6   N1   119.33  3.000
 DJ2  N1   C6   C5   117.89  3.000
 DJ2  N6   C6   C5   122.77  3.000
 DJ2  H1   C8   N9   121.79  3.000
 DJ2  H1   C8   N7   124.81  3.000
 DJ2  N9   C8   N7   113.40  3.000
 DJ2  C2   N1   C6   119.14  3.000
 DJ2  C2   N3   C4   111.68  3.000
 DJ2  H2   C1'  O4'  111.87  3.000
 DJ2  H2   C1'  N9   106.09  3.000
 DJ2  O4'  C1'  N9   109.31  3.000
 DJ2  H2   C1'  C2'  110.07  3.000
 DJ2  N9   C1'  C2'  113.76  3.000
 DJ2  O4'  C1'  C2'  105.85  3.000
 DJ2  H3   C2   N3   116.11  3.000
 DJ2  H3   C2   N1   115.40  3.000
 DJ2  N3   C2   N1   128.48  3.000
 DJ2  H4   C2'  O2'  111.56  3.000
 DJ2  H4   C2'  C3'  109.02  3.000
 DJ2  O2'  C2'  C3'  115.06  3.000
 DJ2  H4   C2'  C1'  109.68  3.000
 DJ2  O2'  C2'  C1'  109.82  3.000
 DJ2  C3'  C2'  C1'  101.17  3.000
 DJ2  H5   C3'  O3'  111.72  3.000
 DJ2  H5   C3'  C4'  111.83  3.000
 DJ2  O3'  C3'  C4'  108.76  3.000
 DJ2  H5   C3'  C2'  111.85  3.000
 DJ2  O3'  C3'  C2'  110.98  3.000
 DJ2  C4'  C3'  C2'  101.21  3.000
 DJ2  H6   C4'  O4'  108.21  3.000
 DJ2  H6   C4'  C5'  109.11  3.000
 DJ2  O4'  C4'  C5'  110.86  3.000
 DJ2  H6   C4'  C3'  110.47  3.000
 DJ2  C5'  C4'  C3'  112.08  3.000
 DJ2  O4'  C4'  C3'  106.01  3.000
 DJ2  H8   C5'  H7   107.01  3.000
 DJ2  H8   C5'  O5'  111.19  3.000
 DJ2  H7   C5'  O5'  111.52  3.000
 DJ2  H8   C5'  C4'  111.20  3.000
 DJ2  H7   C5'  C4'  108.19  3.000
 DJ2  O5'  C5'  C4'  107.73  3.000
 DJ2  H10  N6   H9   118.39  3.000
 DJ2  H10  N6   C6   120.36  3.000
 DJ2  H9   N6   C6   121.21  3.000
 DJ2  C8   N7   C5   104.39  3.000
 DJ2  C1'  N9   C8   127.21  3.000
 DJ2  C1'  N9   C4   126.55  3.000
 DJ2  C8   N9   C4   106.24  3.000
 DJ2  H12  NAA  H11  105.60  3.000
 DJ2  H12  NAA  O5'  104.88  3.000
 DJ2  H11  NAA  O5'  104.85  3.000
 DJ2  H13  O2'  C2'  108.96  3.000
 DJ2  H14  O3'  C3'  107.94  3.000
 DJ2  C4'  O4'  C1'  110.79  3.000
 DJ2  NAA  O5'  C5'  109.51  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 DJ2  CONST_01  C8   N7   C5   C4     0.00   0.0  0
 DJ2  CONST_02  N1   C6   C5   C4     0.00   0.0  0
 DJ2  CONST_03  N7   C8   N9   C4     0.00   0.0  0
 DJ2  CONST_04  N1   C2   N3   C4     0.00   0.0  0
 DJ2  CONST_05  N9   C8   N7   C5     0.00   0.0  0
 DJ2  CONST_06  C2   N1   C6   C5     0.00   0.0  0
 DJ2  CONST_07  C8   N9   C4   C5     0.00   0.0  0
 DJ2  CONST_08  C2   N3   C4   C5     0.00   0.0  0
 DJ2  CONST_09  C8   N7   C5   C6   180.00   0.0  0
 DJ2  CONST_10  N9   C4   C5   C6   180.00   0.0  0
 DJ2  CONST_11  N3   C4   C5   C6     0.00   0.0  0
 DJ2  CONST_12  N3   C2   N1   C6     0.00   0.0  0
 DJ2  CONST_13  N3   C4   N9   C8   180.00   0.0  0
 DJ2  CONST_14  N7   C5   C6   N1   180.00   0.0  0
 DJ2  CONST_15  N7   C5   C4   N3   180.00   0.0  0
 DJ2  CONST_16  N9   C4   N3   C2   180.00   0.0  0
 DJ2  CONST_17  N9   C4   C5   N7     0.00   0.0  0
 DJ2  CONST_18  C1'  N9   C4   C5   180.00   0.0  0
 DJ2  CONST_19  C1'  N9   C4   N3     0.00   0.0  0
 DJ2  CONST_20  N7   C8   N9   C1'  180.00   0.0  0
 DJ2  CONST_21  N6   C6   C5   C4   180.00   0.0  0
 DJ2  CONST_22  N6   C6   N1   C2   180.00   0.0  0
 DJ2  CONST_23  N7   C5   C6   N6     0.00   0.0  0
 DJ2  CONST_24  H1   C8   N9   C4   180.00   0.0  0
 DJ2  CONST_25  H3   C2   N3   C4   180.00   0.0  0
 DJ2  CONST_26  H9   N6   C6   C5     0.00   0.0  0
 DJ2  CONST_27  H10  N6   C6   C5   180.00   0.0  0
 DJ2  Var_01    H11  NAA  O5'  C5'  124.79  30.0  3
 DJ2  Var_02    H7   C5'  O5'  NAA   61.78  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 DJ2  chir_01  C1'  O4'  N9   C2'  negativ
 DJ2  chir_02  C2'  O2'  C1'  C3'  negativ
 DJ2  chir_03  C3'  O3'  C4'  C2'  positiv
 DJ2  chir_04  C4'  O4'  C3'  C5'  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 DJ2  plan-1  C4   0.020
 DJ2  plan-1  C5   0.020
 DJ2  plan-1  C6   0.020
 DJ2  plan-1  C8   0.020
 DJ2  plan-1  N1   0.020
 DJ2  plan-1  N3   0.020
 DJ2  plan-1  C1'  0.020
 DJ2  plan-1  C2   0.020
 DJ2  plan-1  N6   0.020
 DJ2  plan-1  N7   0.020
 DJ2  plan-1  N9   0.020
 DJ2  plan-1  H1   0.020
 DJ2  plan-1  H3   0.020
 DJ2  plan-2  C6   0.020
 DJ2  plan-2  N6   0.020
 DJ2  plan-2  H9   0.020
 DJ2  plan-2  H10  0.020

